[ome-users] FlowSight .cif file opened with low resolution

[Melissa Linkert]

Hi Minh,

Thank you for reporting this problem.

> I'm working on a project that uses Amnis FlowSight .cif , which could be opened by Bioformats (MATLAB version and python-bioformats)
>
> Unfortunately the resolution of the image after being opened by both of the versions are lossy. Can anyone so kind to help me check this out.

I can confirm that Bio-Formats reports images that are approximately
35x35 to 55x55 pixels for the attached
export_to_cif_for_later_tiff.cif.  However, I so far have not been
able to find evidence of higher resolution images in the file.

> I send here 2 screenshots, one that compares between image opened by python-bioformats and its original form (export directly from Amnis IDEAS). And the other screenshot compare image opened by MATLAB-bioformats package, > compared with its original form
>
> I also attach an example .cif file.

>From the screenshots, it looks like export_to_cif_for_later_tiff.cif
is not the file being opened in IDEAS or MATLAB.  Could you please
confirm that the screenshots do indeed represent a different file?  If
so, could you please send a relevant screenshot of
export_to_cif_for_later_tiff.cif being opened/exported in IDEAS?  In
either case, do you have an idea of what the correct X and Y
dimensions should be?  The OME team does not have access to the Amnis
IDEAS software, so any additional information you can provide would be
very helpful for debugging.

Regards,
-Melissa

On Tue, Jan 17, 2017 at 2:40 PM, Minh Doan <minhdoan at broadinstitute.org> wrote:
> Hello all, good afternoon,
>
> I am Minh Doan, a postdoc in imaging platform of Broad Institute. I'm
> working on a project that uses Amnis FlowSight .cif , which could be opened
> by Bioformats (MATLAB version and python-bioformats)
>
> Unfortunately the resolution of the image after being opened by both of the
> versions are lossy. Can anyone so kind to help me check this out.
>
> I send here 2 screenshots, one that compares between image opened by
> python-bioformats and its original form (export directly from Amnis IDEAS).
> And the other screenshot compare image opened by MATLAB-bioformats package,
> compared with its original form
>
> I also attach an example .cif file.
>
> Any advices are very much appreciated.
>
> Bests,
> Minh
>
> --
>
> Minh Doan, M.D., Ph.D.
> Imaging Platform
> Broad Institute of Harvard and MIT
> 415 Main Street,
> Cambridge MA 02142
> phone: (617) 714-7681
> minhdoan at broadinstitute.org
>
>
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